Software for custom 2p scopes

If you build your own two photon scope, you’ll need software. I mainly use the MATLAB-based ScanImage. Vijay Iyer (Janelia Farm) has really made it a slick, stable program. It cosmetically resembles Tom Pologruto’s original work, which is good, but under the hood he has made some excellent improvements. For example, they have written their own NI-DAQmx wrapper for MATLAB, to avoid using MATLAB’s own DAQ Toolbox. This has advantages for speed and stability. Plus, they’re not at the mercy of MathWorks for updates. For example, a talented programmer in our lab recently made a 64-bit version of the wrapper.

I have used some other packages, including MPScope (nice software, but be prepared to write a formal letter of thanks to David before you can even download it to try it) and PrairieView. The latter is only available on Prairie scopes, so it’s not really an option for homebrew systems. However, if you do run a PrairieView system, you might like to know that they’re pretty responsive if you want to interface your own code with their software. This way you can add a feature to PrairieView yourself, without having to start from scratch. There are also several other packages that people sometimes share with other researchers, but do not release to the general public. Ask around if you’re interested in that route.

The latest entry is Sutter’s MCS (MOM Computer System, pictured above). It’s a high-ticket (5 figures) software package that they’re demoing around SfN this year (info@sutter.com). Features include integrated electrophysiology data acquisition, real-time fluorescence time courses, and some offline analysis tools. It will be interesting to see the details.